Release version for Erange 4.0a

[erange.git] / distalPairs.py

diff --git a/distalPairs.py b/distalPairs.py
index 5bc25321b25b8a30e9b09511cabbee4355010b71..be403109110c3fb40f7bba831f6c2ea48e496536 100755 (executable)
--- a/distalPairs.py
+++ b/distalPairs.py
@@ -85,33 +85,17 @@ def distalPairs(minDist, rdsfile, outfilename, sameChromOnly=False, doSplices=Fa
 
     print time.ctime()
 
-    if doSplices:
-        print "getting splices"
-        splicesDict = RDS.getSplicesDict(withChrom=True, withPairID=True, readIDDict=True, splitRead=True)
-        print "got splices"
-
     print "getting uniq reads"    
     uniqDict = RDS.getReadsDict(withChrom=True, withPairID=True, doUniqs=True, readIDDict=True)
     print "got uniqs"
 
     if doSplices:
-        for readID in splicesDict:
-            theRead = splicesDict[readID]
-            read0 = theRead[0]
-            del read0[1]
-            try:
-                uniqDict[readID].append(read0)
-            except:
-                if len(theRead) == 4:
-                    read2 = theRead[2]
-                    del read2[1]
-                    uniqDict[readID] = [read0,read2]
+        addSplicesToUniqReads(RDS, uniqDict)
 
     if doVerbose:
         print len(uniqDict), time.ctime()
 
     outfile = open(outfilename,"w")
-
     diffChrom = 0
     distal = 0
     total = 0
@@ -132,16 +116,15 @@ def distalPairs(minDist, rdsfile, outfilename, sameChromOnly=False, doSplices=Fa
                     continue
                 else:
                     outline = "%s\t%s\t%d\t%s\t%s\t%d\t%s" % (readID, chrom1, start1, sense1, chrom2, start2, sense2)
-                    outfile.write(outline + "\n")
+                    print >> outfile, outline
                     if doVerbose:
                         print diffChrom, outline
             else:
                 dist = abs(start1 - start2)
-
                 if minDist < dist < maxDist:
                     distal += 1
                     outline = "%s\t%s\t%d\t%s\t%d\t%s\t%d" % (readID, chrom1, start1, sense1, start2, sense2, dist)
-                    outfile.write(outline + "\n")
+                    print >> outfile, outline
                     if doVerbose:
                         print distal, outline
 
@@ -157,5 +140,22 @@ def distalPairs(minDist, rdsfile, outfilename, sameChromOnly=False, doSplices=Fa
     print time.ctime()
 
 
+def addSplicesToUniqReads(RDS, uniqDict):
+    print "getting splices"
+    splicesDict = RDS.getSplicesDict(withChrom=True, withPairID=True, readIDDict=True, splitRead=True)
+    print "got splices"
+    for readID in splicesDict:
+        theRead = splicesDict[readID]
+        read0 = theRead[0]
+        del read0[1]
+        try:
+            uniqDict[readID].append(read0)
+        except:
+            if len(theRead) == 4:
+                read2 = theRead[2]
+                del read2[1]
+                uniqDict[readID] = [read0,read2]
+
+
 if __name__ == "__main__":
     main(sys.argv)
\ No newline at end of file